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Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2

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An Erratum to this article was published on 15 August 2010

Abstract

The proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream experiments. Following efficient secretome purification, GeLC-MS2 analysis and prediction servers suggested probable protein secretion to complement experimental data. In an effort to define the extracellular proteome of the extreme thermophilic bacterium Caldicellulosiruptor saccharolyticus, several techniques were considered regarding sample processing to achieve the most in-depth analysis of secreted proteins. Order of operation experiments, all including the C18 bead technique, demonstrated that two levels of sample purification were necessary to effectively desalt the sample and provide sufficient protein identifications. Five sample preparation combinations yielded 71 proteins and the majority described, as enzymatic and putative uncharacterized proteins, anticipate consolidated bioprocessing applications. Nineteen proteins were predicted by Phobius, SignalP, SecretomeP, or TatP for extracellular secretion, and 11 contained transmembrane domain stretches suggested by Phobius and transmembrane hidden Markov model. The sample preparation technique demonstrating the most effective outcome for C. saccharolyticus secreted proteins in this study, involved acetone precipitation followed by the C18 bead method in which 2.4% (63 proteins) of the predicted proteome was identified, including proteins suggested to have secretion and transmembrane moieties.

Experimental workflow for the evaluation of sample cleanup techniques for the secretome of the thermophilic bacterium Caldicellulosiruptor saccharolyticus with possibility to traverse other similarly grown bacterium. Several sample purification methods were assessed individually as well as in combination with a C18 bead method in an effort to afford the greatest number of confidently identified proteins. Analysis of the identified proteins by prediction servers complemented the experimental secretome investigation.

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Acknowledgements

We would like to acknowledge the financial support of the National Institutes of Health (Grant 5T32GM00-8776-08), which supports GLA in the North Carolina State University Molecular Biotechnology Training Program, and the W. M. Keck Foundation. RMK acknowledges support from the US National Science Foundation (CBT0617272) and the Bioenergy Science Center (BESC), a US DOE Bioenergy Research Center supported by the Office of Biological and Environmental Research. DLL acknowledges support from a US Department of Education GAANN Fellowship.

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Authors and Affiliations

  1. North Carolina State University, Raleigh, NC, 27695, USA

    David Muddiman & Genna Andrews

  2. Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA

    Derrick Lewis, Jaspreet Notey & Robert Kelly

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  1. David Muddiman
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  2. Genna Andrews
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Correspondence to David Muddiman.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s00216-010-4102-0

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Muddiman, D., Andrews, G., Lewis, D. et al. Part I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS2 . Anal Bioanal Chem 398, 377–389 (2010). https://doi.org/10.1007/s00216-010-3955-6

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